The national school chaplaincy code of conduct, which every chaplain must sign, stipulates they should not take advantage of their privileged position to try to convert children to their religious belief or denomination.

But on its website, the boss of Access Ministries outlines a strategy to "make students disciples."

Last month, Dr Evonne Paddison strenuously denied Access Ministries' religious teachers or chaplains sought to convert students in state schools.

"We instruct our people not to proselytise, we're not there to convert children," she said.

But that is not what she told a group of Anglican Evangelicals in 2008.

"In Australia, we have a God-given open door to children and young people," she said.

"Our Federal and State Governments allow us to take the Christian faith into schools.

"We need to go and make disciples."

The speech she gave the Anglican Evangelical fellowship is posted on the group's website.

That missionary aim flies in the face of federal guidelines, and federal Education Minister Peter Garrett intends to investigate the matter.

Mr Garrett says it is absolutely crystal clear in the guidelines that it is not about proselytising.

"So if there is any indication or examples of that happening, then my expectation is that that ought to be looked into and investigated by my department," he said.

Mary Bluett from the Australian Education Union is urging the Victorian Education Minister to spend the money elsewhere.

"We'd urge [Education Minister] Martin Dixon here in Victoria to immediately cut the additional $800,000 of funding for Access Ministries that he's put through in this latest budget," she said.